Modern methods of molecular cloning and analysis allow for the detection and amplification of rare DNA sequences such as a single integrated viral segment. Molecular clones of several newly integrated retroviral genomes have been produced in either plasmid or bacteriophage cloning vehicles using recombinant DNA techniques and have been characterized using electron microscope heteroduplex and R-loop methods. Detection of sequence homology even when rearranged or interrupted by intervening cellular DNA is often accurately mappable in the electron microscope using these methods. These studies have not only shown the arrangement of integrated viral sequences within infected host cell DNA, but have also demonstrated the presence and sequence arrangement of certain viral transforming sequences within normal, uninfected host cells as well. These studies have recently been expanded to include a structural determination of the genetic relatedness of AIDS virus isolates from around the world. Unique inverted repeat sequences structurally resembling transposable elements have been identified in the area of retroviral integrations and molecularly cloned for further analysis. The major objective of these studies has been the application of physical and biochemical techniques to assess the influence of integrative position of flanking cellular sequences on subsequent viral function and to define in molecular terms those events which take place during integrative recombination in eukaryotic cell systems.